org.utgenome.gwt.utgb.server
Class BrowserServiceImpl

java.lang.Object
  extended by javax.servlet.GenericServlet
      extended by javax.servlet.http.HttpServlet
          extended by com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
              extended by com.google.gwt.user.server.rpc.RemoteServiceServlet
                  extended by org.utgenome.gwt.utgb.server.BrowserServiceImpl
All Implemented Interfaces:
com.google.gwt.user.client.rpc.RemoteService, com.google.gwt.user.server.rpc.SerializationPolicyProvider, Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig, BrowserService

public class BrowserServiceImpl
extends com.google.gwt.user.server.rpc.RemoteServiceServlet
implements BrowserService

{"species":{"type":0, "target":"human"}, "genome":{"type":0}, "chromosome":{"type":0}}

Author:
leo
See Also:
Serialized Form

Field Summary
 
Fields inherited from class com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
perThreadRequest, perThreadResponse
 
Constructor Summary
BrowserServiceImpl()
           
 
Method Summary
 TrackView createTrackView(String silk)
           
 List<String> getChildDBGroups(String parentDBGroup)
           
 ChrRange getChrRegion(String species, String revision)
           
 List<CompactWIGData> getCompactWigDataList(String path, int windowWidth, ChrLoc location, GraphWindow window)
           
 String getCurrentView()
           
 String getDatabaseCatalog(String jdbcAddress)
           
 String getDataModelParameter(String amoebaQuery)
           
 List<DatabaseEntry> getDBEntry(String dbGroup)
           
 List<String> getDBNames(String dbGroup)
           
 List<Gene> getGeneList(String serviceURI)
           
 String getHTTPContent(String url)
           
 List<Interval> getLocusList(String dbGroup, String dbName, ChrLoc location)
           
 List<GenomeRange> getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config)
          Get read data from the specified DB and location
 String getRefSeq(String refSeqFileName, String rname, int start, int end)
           
 List<SAMRead> getSAMReadList(String readFileName, String refSeqFileName)
           
 String getTableData(String jdbcAddress, String tableName)
           
 List<TrackBean> getTrackList(int entriesPerPage, int page)
           
 List<TrackBean> getTrackList(String prefix, int entriesPerPage, int page)
           
 TrackView getTrackView(String viewName)
           
 List<WigGraphData> getWigDataList(String fileName, int windowWidth, ChrLoc location)
           
 KeywordSearchResult keywordSearch(String species, String revision, String keyword, int numEntriesPerPage, int page)
           
 int numHitsOfTracks(String prefix)
           
 List<SAMRead> querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end)
           
 void saveView(String viewXML)
           
 
Methods inherited from class com.google.gwt.user.server.rpc.RemoteServiceServlet
checkPermutationStrongName, doGetSerializationPolicy, getSerializationPolicy, onAfterResponseSerialized, onBeforeRequestDeserialized, processCall, processPost, shouldCompressResponse
 
Methods inherited from class com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
doPost, doUnexpectedFailure, getPermutationStrongName, getThreadLocalRequest, getThreadLocalResponse, onAfterRequestDeserialized, readContent
 
Methods inherited from class javax.servlet.http.HttpServlet
doDelete, doGet, doHead, doOptions, doPut, doTrace, getLastModified, service, service
 
Methods inherited from class javax.servlet.GenericServlet
destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BrowserServiceImpl

public BrowserServiceImpl()
                   throws org.xerial.db.DBException
Throws:
org.xerial.db.DBException
Method Detail

createTrackView

public TrackView createTrackView(String silk)
                          throws UTGBClientException
Specified by:
createTrackView in interface BrowserService
Throws:
UTGBClientException

getTrackView

public TrackView getTrackView(String viewName)
                       throws UTGBClientException
Specified by:
getTrackView in interface BrowserService
Throws:
UTGBClientException

getDataModelParameter

public String getDataModelParameter(String amoebaQuery)

getHTTPContent

public String getHTTPContent(String url)
Specified by:
getHTTPContent in interface BrowserService

getDatabaseCatalog

public String getDatabaseCatalog(String jdbcAddress)
Specified by:
getDatabaseCatalog in interface BrowserService

getTableData

public String getTableData(String jdbcAddress,
                           String tableName)
Specified by:
getTableData in interface BrowserService

getTrackList

public List<TrackBean> getTrackList(int entriesPerPage,
                                    int page)
Specified by:
getTrackList in interface BrowserService

getTrackList

public List<TrackBean> getTrackList(String prefix,
                                    int entriesPerPage,
                                    int page)
Specified by:
getTrackList in interface BrowserService

numHitsOfTracks

public int numHitsOfTracks(String prefix)
Specified by:
numHitsOfTracks in interface BrowserService

keywordSearch

public KeywordSearchResult keywordSearch(String species,
                                         String revision,
                                         String keyword,
                                         int numEntriesPerPage,
                                         int page)
                                  throws UTGBClientException
Specified by:
keywordSearch in interface BrowserService
Throws:
UTGBClientException

saveView

public void saveView(String viewXML)

getCurrentView

public String getCurrentView()

getGeneList

public List<Gene> getGeneList(String serviceURI)

getChrRegion

public ChrRange getChrRegion(String species,
                             String revision)
Specified by:
getChrRegion in interface BrowserService

getLocusList

public List<Interval> getLocusList(String dbGroup,
                                   String dbName,
                                   ChrLoc location)

getChildDBGroups

public List<String> getChildDBGroups(String parentDBGroup)
Specified by:
getChildDBGroups in interface BrowserService

getDBNames

public List<String> getDBNames(String dbGroup)
Specified by:
getDBNames in interface BrowserService

getDBEntry

public List<DatabaseEntry> getDBEntry(String dbGroup)
Specified by:
getDBEntry in interface BrowserService

getWigDataList

public List<WigGraphData> getWigDataList(String fileName,
                                         int windowWidth,
                                         ChrLoc location)
Specified by:
getWigDataList in interface BrowserService

getCompactWigDataList

public List<CompactWIGData> getCompactWigDataList(String path,
                                                  int windowWidth,
                                                  ChrLoc location,
                                                  GraphWindow window)
Specified by:
getCompactWigDataList in interface BrowserService

getSAMReadList

public List<SAMRead> getSAMReadList(String readFileName,
                                    String refSeqFileName)
Specified by:
getSAMReadList in interface BrowserService

querySAMReadList

public List<SAMRead> querySAMReadList(String bamFileName,
                                      String indexFileName,
                                      String refSeqFileName,
                                      String rname,
                                      int start,
                                      int end)
Specified by:
querySAMReadList in interface BrowserService

getRefSeq

public String getRefSeq(String refSeqFileName,
                        String rname,
                        int start,
                        int end)
Specified by:
getRefSeq in interface BrowserService

getOnGenomeData

public List<GenomeRange> getOnGenomeData(GenomeDB db,
                                         ChrLoc range,
                                         ReadQueryConfig config)
Description copied from interface: BrowserService
Get read data from the specified DB and location

Specified by:
getOnGenomeData in interface BrowserService
Parameters:
db - database to search
range - (chr, start, end)
Returns:


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